[English] 日本語
Yorodumi
- PDB-6ix3: The structure of LepI complex with SAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ix3
TitleThe structure of LepI complex with SAM
ComponentsO-methyltransferase lepI
KeywordsBIOSYNTHETIC PROTEIN / Leporin / SAM / O-methyltransferase / Pericyclase
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsCai, Y. / Ohashi, M. / Hai, Y. / Tang, Y. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB20000000 China
CitationJournal: Nat.Chem. / Year: 2019
Title: Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.
Authors: Cai, Y. / Hai, Y. / Ohashi, M. / Jamieson, C.S. / Garcia-Borras, M. / Houk, K.N. / Zhou, J. / Tang, Y.
History
DepositionDec 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8165
Polymers90,9832
Non-polymers8323
Water8,053447
1
A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules

A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,63110
Polymers181,9674
Non-polymers1,6656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22110 Å2
ΔGint-187 kcal/mol
Surface area59560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.301, 61.792, 113.318
Angle α, β, γ (deg.)90.00, 113.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein O-methyltransferase lepI / Leporins biosynthesis protein I


Mass: 45491.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: lepI, AFLA_066940 / Production host: Escherichia coli (E. coli)
References: UniProt: B8NJH3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium chloride, 0.1M MES(pH 6.0), 20%(w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 56044 / % possible obs: 97.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 19.553
Reflection shellResolution: 2.13→2.18 Å / Rmerge(I) obs: 2.028 / Num. unique obs: 2744

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXv1.12_2829phasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→36.959 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.2114 2834 5.09 %
Rwork0.1756 --
obs0.1774 55671 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→36.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6103 0 55 447 6605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046444
X-RAY DIFFRACTIONf_angle_d0.7758781
X-RAY DIFFRACTIONf_dihedral_angle_d26.7832425
X-RAY DIFFRACTIONf_chiral_restr0.043976
X-RAY DIFFRACTIONf_plane_restr0.0061150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.16670.25941030.20532096X-RAY DIFFRACTION78
2.1667-2.20610.27881670.19912581X-RAY DIFFRACTION95
2.2061-2.24850.23341340.19772553X-RAY DIFFRACTION96
2.2485-2.29440.22691160.19652678X-RAY DIFFRACTION97
2.2944-2.34430.25111630.19142615X-RAY DIFFRACTION97
2.3443-2.39880.24341330.18922676X-RAY DIFFRACTION97
2.3988-2.45880.23111460.18712621X-RAY DIFFRACTION97
2.4588-2.52520.25271270.18772672X-RAY DIFFRACTION98
2.5252-2.59950.24211350.19372652X-RAY DIFFRACTION98
2.5995-2.68340.22111340.18962694X-RAY DIFFRACTION98
2.6834-2.77930.21911560.18822656X-RAY DIFFRACTION98
2.7793-2.89050.22981460.18572659X-RAY DIFFRACTION98
2.8905-3.0220.21751220.18842680X-RAY DIFFRACTION98
3.022-3.18130.21981430.18232698X-RAY DIFFRACTION99
3.1813-3.38040.23241500.1852677X-RAY DIFFRACTION99
3.3804-3.64120.20451560.16972720X-RAY DIFFRACTION99
3.6412-4.00730.19241580.15532675X-RAY DIFFRACTION99
4.0073-4.58620.1751530.13942729X-RAY DIFFRACTION99
4.5862-5.77460.18841370.16412754X-RAY DIFFRACTION99
5.7746-36.96490.17291550.16622751X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -34.169 Å / Origin y: -17.9213 Å / Origin z: 25.8129 Å
111213212223313233
T0.1582 Å20.0036 Å2-0.023 Å2-0.1216 Å20.0571 Å2--0.1043 Å2
L1.7839 °2-0.4938 °2-0.4324 °2-0.4521 °20.0867 °2--0.5415 °2
S0.0088 Å °0.2223 Å °0.1196 Å °-0.0187 Å °-0.0415 Å °-0.0049 Å °-0.0321 Å °-0.0781 Å °0.0351 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more